If you are looking for an online reading remediation program, with structured, sequential instruction beginning from phonological awareness and working its way up to comprehension, I believe there is a very short list, which includes Lexia:
http://www.lexiaforhome.com/http://www.rosettastone.com/homeschool/readingThey have an adolescent version, for remediation, which has a more age-appropriate interface, but the material should be the same in both versions, and you can license LexiaCore5 for home. That's only available to schools, though.
I have heard that the program is not quite as good as it was before Rosetta Stone purchased it, but it's still one of the few OG-influenced reading remediation software/webware packages out there that has a decent amount of evidentiary backing. And access to Rosetta Stone's platforms probably makes it easier to use.